MicroRNAome

ABSTRACT

MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. The public miRNA database contains 321 human miRNA sequences, 234 of which have been experimentally verified. To explore the possibility that additional miRNAs are present in the human genome, we have developed an experimental approach called miRNA serial analysis of gene expression (miRAGE) and used it to perform the largest experimental analysis of human miRNAs to date. Sequence analysis of 273,966 small RNA tags from human colorectal cells allowed us to identify 200 known mature miRNAs, 133 novel miRNA candidates, and 112 previously uncharacterized miRNA* forms. To aid in the evaluation of candidate miRNAs, we disrupted the Dicer locus in three human colorectal cancer cell lines and examined known and novel miRNAs in these cells. The miRNAs are useful to diagnose and treat cancers.

This invention was made using funds from the U.S. National Institutes of Health under grant no. CA 43460. Under terms of the grant, the United States Government retains certain rights in the invention.

TECHNICAL FIELD OF THE INVENTION

This invention is related to the area of microRNAs. In particular, it relates to the use of microRNAs for the diagnosis and treatment of cancer.

BACKGROUND OF THE INVENTION

MicroRNAs (miRNAs) are ≈22-nt noncoding RNAs that are processed from larger (≈80-nt) precursor hairpins by the RNase III enzyme Dicer into miRNA:miRNA* duplexes (1-3). One strand of these duplexes associates with the RNA-induced silencing complex (RISC), whereas the other is generally degraded (1). The miRNA-RISC complex targets messenger RNAs for translational repression or mRNA cleavage. There has been considerable debate about the total number of miRNAs that are encoded in the human genome. Initial estimates, relying mostly on evolutionary conservation, suggested there were up to 255 human miRNAs (4). More recent analyses have demonstrated there are numerous nonconserved human miRNAs and suggest this number may be significantly larger (5).

Both cloning and bioinformatic approaches have been used to identify miRNAs. Direct miRNA cloning strategies identified many of the initial miRNAs and demonstrated that miRNAs are found in many species (6-16). However, the throughput of this approach is low, and cloning approaches have appeared to approach saturation (8). Bioinformatic strategies have recently been used to identify potential miRNAs predicted on the basis of various sequence and structural characteristics (4, 7). However, such gene predictions may not point to all legitimate miRNAs, especially those that are not phylogenetically conserved, and all in silico predictions require independent experimental validation.

There is a continuing need in the art to identify additional miRNAs and to exploit their regulatory functions for human health.

SUMMARY OF THE INVENTION

One aspect of the invention is a composition comprising an isolated DNA or RNA polynucleotide comprising a sequence of approximately 18-26 nucleotides having a sequence of a miRNA shown in Table 5 or the complement of a sequence shown in Table 5 or a sequence which is at least 80% identical to said miRNA or complement.

Another aspect of the invention is a pharmaceutical composition comprising an isolated DNA or RNA polynucleotide. The polynucleotide comprises a sequence of approximately 18-26 nucleotides of a miRNA shown in Table 3 or Table 5 or the complement of a sequence shown in Table 3 or Table 5. The isolated DNA or RNA polynucleotide is between 18 and 200 nucleotides inclusive. The polynucleotide may optionally be in a sterile and pyrogen-free vehicle suitable for injection into a human.

Yet another aspect of the invention is an isolated cell line comprising homozygous RNaseIII enzyme Dicer-deficient human cells. The cells display a hypomorphic phenotype. The helicase domain of RNaseIII enzyme Dicer is disrupted.

Still another embodiment of the invention is a pair of isogenic cells. The first cell of said pair of cells is a homozygous RNaseIII enzyme Dicer-deficient human cell which displays a hypomorphic phenotype. The helicase domain of RNaseIII enzyme Dicer of the first cell is disrupted. The second cell is homozygous RNaseIII enzyme Dicer-proficient.

Another embodiment of the invention provides a method of diagnosing a cancer in a patient. The presence of an miRNA or miRNA precursor is detected in a body fluid or tumor specimen from the patient. The miRNA or miRNA precursor is expressed in tumor tissue or cell lines but not in normal tissue, as shown in Table 5. A cancer is identified in the patient when the miRNA or miRNA precursor is detected in the body fluid or tumor specimen from the patient.

Another aspect of the invention is a method of diagnosing a cancer in a patient. Presence or absence of an miRNA or its precursor in a body fluid or tumor specimen from the patient is detected by assaying. The miRNA or its precursor is one which is expressed in normal tissue but not in tumor tissue or cell lines, as shown in Table 5. A cancer in the patient is identified when absence of the miRNA is detected in the body fluid or tumor specimen.

According to one embodiment of the invention a method of diagnosing a colorectal cancer is provided. A miRNA selected from those shown in Table 3 or Table 5 is detected in a test sample of a human and in a normal sample. The amount detected in the test sample is compared to that detected in the normal sample. A ratio of less than 0.7 or greater than 1.4 indicates a colorectal cancer in the human.

According to another embodiment of the invention a method is provided for treating a colorectal cancer in a human. (a) an miRNA selected from those shown in Table 3 with a tumor to normal ratio of less than 0.7; or (b) an miRNA* selected from those shown in Table 3 with a tumor to normal ratio of greater than 1.4 is delivered to the human. Growth of the tumor is thereby arrested, slowed, or reversed.

Still another aspect of the invention is a method of experimentally validating a candidate miRNA. Generation of the candidate miRNA is determined in an isogenic pair of cells which differ in the dicer locus, wherein a first of the pair of cells is hypomorphic for RNaseIII enzyme Dicer activity and a second of the pair of cells has wild-type RNaseIII enzyme Dicer activity. The determined generation of the candidate miRNA in the first of the pair of cells is compared to the determined generation of the candidate miRNA in the second of the pair of cells. A statistically significant reduction of generation of the candidate miRNA in the first relative to the second provides experimental validation that the candidate miRNA is a physiologically relevant miRNA.

Still another embodiment of the invention provides a method of screening for test agents which affect miRNA generation. A test agent is contacted with a cancer cell. Generation of an miRNA in the cancer cell contacted with the test agent is determined. The miRNA is one whose generation is increased or decreased in cancer cells relative to normal cells. The determined generation of the miRNA in the cells contacted with the test agent is compared to generation of the miRNA in cells not contacted with the test agent. A test agent is identified as a potential therapeutic agent if it increases the amount of an miRNA whose generation is decreased in cancer cells or if it decreases the amount of an miRNA whose generation is increased in cancer cells.

According to yet another aspect of the invention a method is provided for identifying candidate agents that target a biosynthetic pathway for generating miRNA molecules or that target generation of an miRNA molecule. A test agent is contacted with a pair of isogenic cells as described above. Generation of an miRNA in the first and second isogenic cells contacted with the test agent is compared to generation of the miRNA in the first and second cells not contacted with the test agent. A test agent is identified as a candidate for affecting the biosynthetic pathway for generating miRNA molecules or generation of the miRNA if the test agent significantly affects generation of the miRNA in the second cell but not in the first cell.

According to another embodiment a method is provided of inhibiting expression of a target gene in a cell. A nucleic acid as described above is introduced into the cell in an amount sufficient to inhibit expression of the target gene. The target gene comprises a binding site substantially identical to a binding site as shown in Table 10 and SEQ ID NOS: 1652-1874.

According to another embodiment, a method is provided of increasing expression of a target gene in a cell. A nucleic acid as described above is introduced into the cell in an amount sufficient to increase expression of the target gene. The target gene comprises a binding site substantially identical to a binding site as shown in Table 10 and SEQ ID NOS: 1652-1874.

Yet another embodiment of the invention provides a method of treating a patient with a disorder listed in Table 9. A composition comprising a nucleic acid as described above is administered to the patient. The symptoms of the disorder are thereby ameliorated.

These and other embodiments which will be apparent to those of skill in the art upon reading the specification provide the art with new tools for diagnosis and therapy of cancer.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. miRAGE approach for isolation of miRNAs. (A) Schematic of miRAGE method. The approach involves isolation of small RNA species (red ovals), followed by ligation of specialized linkers (white rectangles) that enable robust RT-PCR with biotinylated primers (blue circles). Linkers are enzymatically cleaved and removed by binding to streptavidin-coated magnetic beads (yellow ovals). Released tags are concatenated, cloned, and sequenced. (B) Bioinformatic analyses of miRAGE tags. Tags were grouped together based on a 12-bp internal core sequence. The most highly represented tag in each group was then compared to various RNA databases. Tags not matching known RNA sequences were compared to the human genome and analyzed for precursors with thermodynamically stable hairpin structures.

FIG. 2. Clustering of miRNAs in the human genome. Analysis of all 133 miRNAs identified 15 that were near other known or novel miRNAs. Yellow boxes represent candidate miRNAs, whereas white boxes represent known miRNAs. Position coordinates are based on National Center for Biotechnology Information Genome Build 35/University of California, Santa Cruz May 2004 assembly.

FIG. 3. Validation of 133 candidate human miRNAs. A total of 133 miRNA candidates fulfilled expression and biogenesis criteria (black circle). Additional levels of validation include phylogenetically conserved precursor structures (blue circle), multiple observations of expression (red circle), genomic clustering (yellow circle), observation of corresponding miRNA* forms (green circle), and strong homology to known miRNAs (pink circle).

FIG. 4. Disruption of human DICER1 helicase domain in colorectal cancer cells. (A) The endogenous locus is shown together with an AAV-Neo targeting construct for insertion into exon 5 of DICER1. HA, homology arm; P, SV40 promoter; Neo, geneticin-resistance gene; R-ITR and L-ITR are right and left inverted terminal repeats; triangles, loxP sites. (B) PCR analysis of parental (+/+), heterozygous (+/Ex5), and homozygous (Ex5/Ex5) clones from DLD1, HCT116, and RKO colorectal cancer cell lines. Primers used for PCR analysis (P1 and P2) are indicated above the endogenous locus in A.

FIG. 5. miRNA expression in colorectal cancer cells with Dicer disruption. (A) Northern blot analyses show decreased mature miRNAs and increased levels of miRNA precursors in Dicer^(ex5) (Ex5) compared with Dicer wild-type (WT) cells using probes for miR-21 and miR-590. (B) Expression levels of known miRNAs as determined by primer-extension quantitative PCR (PE-qPCR), as described (33). For each graph, pairwise comparisons are displayed showing the ratio of expression in Dicer^(ex5) to WT clones of each cell type.

FIG. 6. Discovery of known and novel miRNAs using miRAGE. Each point represents the average number of known or novel miRNAs (y axis) that were identified by analysis of three simulated subsets comprising the number of miRAGE tags indicated (x axis).

FIG. 7. qRT-PCR expression validation of miRNA candidates. Expression of miRNAs was analyzed in total RNA derived from colon tumor tissue (TUM); adjacent normal colonic epithelial tissue (NAT); pooled colorectal tumor cell lines HCT116, DLD-1, and RKO (Colon lines); pooled extra-colonic tissue from brain, cervix, thymus, and skeletal muscle (Tissue pool); and a no template control (NTC). The lower band present in all NTC lanes represents primer dimers.

FIG. 8. (Table 1.) Evaluation of differentially expressed candidate miRNAs by miRAGE.

FIG. 9. (Table 2.) miRAGE tags of known miRNAs observed in colorectal cells (SEQ ID NO: 1-200).

FIG. 10. (Table 3.) Differential expression of known miRNAs in tumor versus normal tissue.

FIG. 11. (Table 4.) miRNA* forms in colorectal cells (SEQ ID NO: 201-336).

FIG. 12. (Table 5.) One hundred thirty-three candidate novel miRNAs: structure, validation, expression, and genomic organization (SEQ ID NO: 337-469 for mature miRNAs and SEQ ID NO: 1386-1518 for precursor miRNAs).

FIG. 13. (Table 6.) Microarray expression validation of selected miRNA candidates and known miRNAs (SEQ ID NO:470-909 for miRNAs and SEQ ID NO: 910-1349 for probes)

FIG. 14. (Table 7.) qRT-PCR validation of selected miRNA candidates (SEQ ID NO: 1350-1385 for tags).

FIG. 15. (Table 8.) Differential expression of known miRNAs in DicerEx5 versus WT.

FIG. 16. (Table 9.) Provides the corresponding DNA sequence for the 133 novel miRNAs, the name of the target gene that each regulates, the identifier code for the binding sequence within the target gene (the identifier code and the binding sequence are identified in Table 10), and the identifier code for the disease which is associated with misregulation of the target gene (the identifier code and the disease are identified in Table 11). The DNA sequences of the 133 novel miRNAs are shown in SEQ ID NO: 1519-1651.

FIG. 17 (Table 10.) Identifies the binding sequence identifier code and the corresponding binding sequence. These are shown in SEQ ID NO: 1652-1874.

FIG. 18 (Table 11.) Identifies the disease identifier code and the corresponding disease.

DETAILED DESCRIPTION OF THE INVENTION

To increase the efficiency of discovery of small RNA species, the inventors have developed an approach called miRNA serial analysis of gene expression (miRAGE). This approach combines aspects of direct miRNA cloning and SAGE (17). Similar to traditional cloning approaches, miRAGE starts with the isolation of 18- to 26-base RNA molecules to which specialized linkers are ligated, and which are reverse-transcribed into cDNA (FIG. 1A). However, subsequent steps, including amplification of the complex mixture of cDNAs using PCR, tag purification, concatenation, cloning, and sequencing, have been performed by using SAGE methodology optimized for small RNA species. This approach has the advantage of generating large concatemers that can be used to identify as many as 35 tags in a single sequencing reaction, whereas existing cloning protocols analyze on average approximately five miRNAs per reaction (8).

The inventors have found many new miRNA species and have found that many of these as well as many previously described miRNA species are differentially expressed between colorectal cancer cells and in normal cells. Thus these miRNA species can be used inter alia diagnostically to differentiate between cancer and normal cells. In order to identify clear and statistically significant differences, one can set limits on the ratio of expression of such species in cancer to normal. A ratio of less than 0.7 or greater than 1.4 of test sample to normal can be used. More stringent ratios which can can be used are less than 0.6 or greater than 1.5, less than 0.5 or greater than 1.6, less than 0.4 or greater than 1.7. More lenient ratios which can be used include less than 0.8 or greater than 1.3, less than 0.9 or greater than 1.2. Moreover, if an miRNA species is not expressed in normal tissue or cells but is expressed in cancer cells or tissues, then its detection in test tissue or cells is indicative of cancer.

miRNAs can also be used to assess the effects of drugs and drug candidates on miRNA metabolism and generation pathways. Each can be used individually or cumulatively to confirm the effect of a drug or drug candidate on miRNA metabolism generally and on the extent of the effects of a drug or drug candidate. Some drugs or drug candidates may only affect a subset of miRNAs whereas some may affect such metabolism globally.

Test samples from patients having or suspected of having tumors, especially colorectal tumors, can be obtained from biopsies, body fluids (e.g., urine, blood, serum, plasma, tears, saliva) or stool. miRNA species can be detected using hybridization based techniques, such as microarrays, primer extension, PCR, and others.

The miRNAs and their complements (miRNA*s) which are identified herein as differentially expressed, see especially Table 3 and/or Table 5, can be used therapeutically. Either a miRNA or a miRNA precursor or a miRNA* can be delivered to a human with cancer, e.g., colorectal cancer. If the particular miRNA is overexpressed in cancer (relative to normal) then the complement or miRNA* can be administered. If the miRNA is underexpressed in cancer, then the miRNA or its precursor (hairpin loop structure) can be administered. Methods for delivering therapeutic RNA molecules are known in the art and any can be used. Optionally the miRNAs or miRNA*s, or precursors can be formulated in a sterile and pyrogen-free vehicle that is suitable for injection into a human. Such polynucleotides can between about 17 and 250 nucleotides and will contain the sequence of an miRNA or its complement, consisting of between about 17 and 26 nucleotides. The size of the polynucleotide can be at least 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides. The size of the polynucleotide can be less than 225, 200, 175, 150, 125, 100, 75, 50, 40, or 30 nt, for example. The polynucleotide can also be used in a DNA form (having the same base sequence, substituting thymines for uracils).

The miRNAs and their complements (miRNA*s) which are identified herein as differentially expressed can also be used as probes or primers for detection and diagnosis. When used in a hybridization mode, probes or primers can be at least about 80, 82, 84, 86, 88, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to the miRNAs as disclosed here. A small amount of allelic variation is common among members of a species and a small amount of non-identical nucleotides in a probe or primer with typically not prevent hybridization. Probes and primers may be labeled, or may not be. They can be tethered to another substance or they may be tetherable to another substance for detection purposes. The arts of hybridization and amplification and detection are very well developed and many variations are known in how these are actually carried out.

The inventors have also developed hypomorphic mutant cell lines for the RNaseIII enzyme Dicer. These cell lines can be in any genetic background of a human cell, however, advantageously cancer cell lines, such as HCT116, DLD1, RKO, CACO-2, and SW480, can be used. Hypomorphic Dicer phenotype cell lines have disruptions in exon 5. Pairs of isogenic cell lines comprising such hypomorphic Dicer cell lines and their isogenic parents can also be used advantageously for substance screening. The isogenic cell lines can be packaged together in a common container, but will typically be kept in separate vessels so that they will not be mixed. As described in the experimental section below, the isogenic cell lines can also be used to confirm and validate the biological relevance of a candidate miRNA. If a miRNA species is dependent (totally or partially) on Dicer for its expression, then it is highly likely to be a physiological or biologically relevant miRNA.

MicroRNA. A gene coding for a miRNA may be transcribed leading to production of an miRNA precursor known as the pri-miRNA. The pri-miRNA may be part of a polycistronic RNA comprising multiple pri-miRNAs. The pri-miRNA may form a hairpin with a stem and loop. The stem may comprise mismatched bases.

The hairpin structure of the pri-miRNA may be recognized by Drosha, which is an RNase III endonuclease. Drosha may recognize terminal loops in the pri-miRNA and cleave approximately two helical turns into the stem to produce a 60-70 nt precursor known as the pre-miRNA. Drosha may cleave the pri-miRNA with a staggered cut typical of RNase III endonucleases yielding a pre-miRNA stem loop with a 5′ phosphate and −2 nucleotide 3′ overhang. Approximately one helical turn of stem (˜10 nucleotides) extending beyond the Drosha cleavage site may be essential for efficient processing. The pre-miRNA may then be actively transported from the nucleus to the cytoplasm by Ran-GTP and the export receptor Ex-portin-5.

The pre-miRNA may be recognized by Dicer, which is also an RNase III endonuclease. Dicer may recognize the double-stranded stein of the pre-miRNA. Dicer may also recognize the 5′ phosphate and 3′ overhang at the base of the stem loop. Dicer may cleave off the terminal loop two helical turns away from the base of the stem loop leaving an additional 5′ phosphate and −2 nucleotide 3′ overhang. The resulting siRNA-like duplex, which may comprise mismatches, comprises the mature miRNA and a similar-sized fragment known as the miRNA*.

The miRNA and miRNA* may be derived from opposing arms of the pri-miRNA and pre-miRNA. MiRNA* sequences may be found in libraries of cloned miRNAs but typically at lower frequency than the miRNAs.

Although initially present as a double-stranded species with miRNA*, the miRNA may eventually become incorporated as single-stranded RNAs into a ribonucleoprotein complex known as the RNA-induced silencing complex (RISC). Various proteins can form the RISC, which can lead to variability in specificity for miRNA/miRNA* duplexes, binding site of the target gene, activity of miRNA (repress or activate), which strand of the miRNA/miRNA* duplex is loaded in to the RISC.

When the miRNA strand of the miRNA:miRNA* duplex is loaded into the RISC, the miRNA* may be removed and degraded. The strand of the miRNA:miRNA* duplex that is loaded into the RISC may be the strand whose 5′ end is less tightly paired. In cases where both ends of the miRNA:miRNA* have roughly equivalent 5′ pairing, both miRNA and miRNA* may have gene silencing activity.

The RISC may identify target nucleic acids based on high levels of complementarity between the miRNA and the mRNA, especially by nucleotides 2-8 of the miRNA. Only one case has been reported in animals where the interaction between the miRNA and its target was along the entire length of the miRNA. This was shown for mir-196 and Hox B8 and it was further shown that mir-196 mediates the cleavage of the Hox B8 mRNA (Yekta et al 2004, Science 304-594). Otherwise, such interactions are known only in plants (Bartel & Bartel 2003, Plant Physiol 132-709).

A number of studies have looked at the base-pairing requirement between miRNA and its mRNA target for achieving efficient inhibition of translation (reviewed by Bartel, 2004, Cell 116-281). In mammalian cells, the first 8 nucleotides of the miRNA may be important (Doench & Sharp 2004 GenesDev 2004-504). However, other parts of the microRNA may also participate in mRNA binding. Moreover, sufficient base pairing at the 3′ can compensate for insufficient pairing at the 5′ (Brennecke at al, 2005 PLoS 3-e85). Computation studies, analyzing miRNA binding on whole genomes have suggested a specific role for bases 2-7 at the 5′ of the miRNA in target binding but the role of the first nucleotide, found usually to be “A” was also recognized (Lewis et at 2005 Cell 120-15). Similarly, nucleotides 1-7 or 2-8 were used to identify and validate targets by Krek et al (2005, Nat Genet 37-495).

The target sites in the mRNA may be in the 5′ UTR, the 3′ UTR or in the coding region. Interestingly, multiple miRNAs may regulate the same mRNA target by recognizing the same or multiple sites. The presence of multiple miRNA complementarity sites in most genetically identified targets may indicate that the cooperative action of multiple RISCs provides the most efficient translational inhibition.

MicroRNAs may direct the RISC to downregulate gene expression by either of two mechanisms: mRNA cleavage or translational repression. The miRNA may specify cleavage of the mRNA if the mRNA has a certain degree of complementarity to the miRNA. When a miRNA guides cleavage, the cut may be between the nucleotides pairing to residues 10 and 11 of the miRNA. Alternatively, the miRNA may repress translation if the miRNA does not have the requisite degree of complementarity to the miRNA.

There may be variability in the 5′ and 3′ ends of any pair of miRNA and miRNA*. This variability may be due to variability in the enzymatic processing of Drosha and Dicer with respect to the site of cleavage. Variability at the 5′ and 3′ ends of miRNA and miRNA* may also be due to mismatches in the stem structures of the pri-miRNA and pre-miRNA. The mismatches of the stem strands may lead to a population of different hairpin structures. Variability in the stem structures may also lead to variability in the products of cleavage by Drosha and Dicer.

Nucleic Acid.

A nucleic acid variant may be a complement of the referenced nucleotide sequence. The variant may also be a nucleotide sequence that is substantially identical to the referenced nucleotide sequence or the complement thereof. The variant may also be a nucleotide sequence which hybridizes under stringent conditions to the referenced nucleotide sequence, complements thereof, or nucleotide sequences substantially identical thereto. The nucleic acid may have a length of from 10 to 250 nucleotides. The nucleic acid may have a length of at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80 or 90 nucleotides and a length of less than 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80 or 90 nucleotides. The nucleic acid may be synthesized or expressed in a cell (in vitro or in vivo) using a synthetic gene described below. The nucleic acid may be synthesized as a single strand molecule and hybridized to a substantially complementary nucleic acid to form a duplex, which is also considered a nucleic acid of the invention. The nucleic acid may be introduced into a cell, tissue or organ in a single- or double-stranded form or capable of being expressed by a synthetic gene using methods well known to those skilled in the art, including as described in U.S. Pat. No. 6,506,559 which is incorporated by reference.

Pri-miRNA

The nucleic acid of the invention may comprise a sequence of a pri-miRNA or a variant thereof. The pri-miRNA sequence may comprise from 45-30,000 nucleotides, with examples of lengths of 45-250, 55-200, 70-150, 80-100, 45-90, 60-80, and 60-70 nucleotides. The sequence of the pri-miRNA may comprise a pre-miRNA, miRNA and miRNA* as set forth below. The pri-miRNA may also comprise a miRNA or miRNA* and the complement thereof, and variants thereof The pri-miRNA may comprise at least 19% adenosine nucleotides, at least 16% cytosine nucleotides, at least 23% thymine nucleotides and at least 19% guanine nucleotides.

The pri-miRNA may form a hairpin structure. The hairpin may comprise a first and second nucleic acid sequence that are substantially complimentary. The first and second nucleic acid sequence may be from 30-200 nucleotides. The first and second nucleic acid sequence may be separated by a third sequence of from 8-12 nucleotides. The hairpin structure may have a free energy less than −25 Kcal/mole as calculated by the Vienna algorithm with default parameters, as described in Hofacker et al., Monatshefte f. Chemie 125: 167-188 (1994), the contents of which are incorporated herein. The hairpin may comprise a terminal loop of, for example, 4-20, 8-12 or 10 nucleotides.

MiRNA

The nucleic acid of the invention may also comprise a sequence of a miRNA, miRNA* or a variant thereof. The miRNA sequence may comprise from 13-33, 18-24 or 21-23 nucleotides. The sequence of the miRNA may be the first 13-33 nucleotides of the pre-miRNA. The sequence of the miRNA may be the last 13-33 nucleotides of the pre-miRNA.

Anti-miRNA

The nucleic acid of the invention may also comprise a sequence of an anti-miRNA that is capable of blocking the activity of a miRNA or miRNA*. The anti-miRNA may comprise a total of 5-100 or 10-60 nucleotides. The anti-miRNA may also comprise a total of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides. The sequence of the anti-miRNA may comprise (a) at least 5 nucleotides that are substantially identical to the 5′ of a miRNA and at least 5-12 nucleotide that are substantially complimentary to the flanking regions of the target site from the 5′ end of said miRNA, or (b) at least 5-12 nucleotides that are substantially identical to the 3′ of a miRNA and at least 5 nucleotide that are substantially complimentary to the flanking region of the target site from the 3′ end of the miRNA. The sequence of the anti-miRNA may comprise the compliment of a sequence of a miRNA disclosed herein or variants thereof.

Binding Site of Target

The nucleic acid of the invention may also comprise a sequence of a target miRNA binding site, or a variant thereof. The target site sequence may comprise a total of 5-100 or 10-60 nucleotides. The target site sequence may comprise at least 5 nucleotides of the sequence of a target gene binding site or variants thereof.

Synthetic Gene

The present invention also relates to a synthetic gene comprising a nucleic acid of the invention operably linked to transcriptional and/or translational regulatory sequences. The synthetic gene may be capable of modifying the expression of a target gene with a binding site for the nucleic acid of the invention. Expression of the target gene may be modified in a cell, tissue or organ. The synthetic gene may be synthesized or derived from naturally-occurring genes by standard recombinant techniques. The synthetic gene may also comprise terminators at the 3′-end of the transcriptional unit of the synthetic gene sequence. The synthetic gene may also comprise a selectable marker.

Vectors.

The present invention also relates to a vector comprising a synthetic gene of the invention. The vector may be an expression vector. An expression vector may comprise additional elements. For example, the expression vector may have two replication systems allowing it to be maintained in two organisms, e.g., in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. For integrating expression vectors, the expression vector may contain at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. The vector may also comprise a selectable marker gene to allow the selection of transformed host cells. Host cells comprising a vector may be a bacterial, fungal, plant, insect or mammalian cell.

Probes.

Probes may be used for screening and diagnostic methods, as outlined below. The probe may be attached or immobilized to a solid substrate, such as a microarray. The probe may have a length of from 8 to 500, 10 to 100, or 20 to 60 nucleotides. The probe may also have a length of at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 120,140, 160, 180, 200, 220, 240, 260, 280 or 300 nucleotides and/or less than 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 120,140, 160, 180, 200, 220, 240, 260, 280 or 300 nucleotides. The probe may further comprise a linker sequence of from 10-60 nucleotides.

Microarray

A microarray may comprise a solid substrate comprising an attached probe or plurality of probes of the invention. The probes may be capable of hybridizing to a target sequence under stringent hybridization conditions. The probes may be attached at spatially defined address on the substrate. More than one probe per target sequence may be used, with either overlapping probes or probes to different sections of a particular target sequence. The probes may be capable of hybridizing to target sequences associated with a single disorder. The probes may be attached to the microarray in a wide variety of ways, as will be appreciated by those in the art. The probes may either be synthesized first, with subsequent attachment to the microarray, or may be directly synthesized on the microarray.

The solid substrate may be a material that may be modified to contain discrete individual sites appropriate for the attachment or association of the probes and is amenable to at least one detection method. Representative examples of substrates include glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, TeflonJ, etc.), polysaccharides, nylon or nitrocellulose, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses and plastics. The substrates may allow optical detection without appreciably fluorescing. The substrate may be planar, although other configurations of substrates may be used as well. For example, probes may be placed on the inside surface of a tube, for flow-through sample analysis to minimize sample volume. Similarly, the substrate may be flexible, such as a flexible foam, including closed cell foams made of particular plastics.

The microarray and the probe may be derivatized with chemical functional groups for subsequent attachment of the two. For example, the microarray may be derivatized with a chemical functional group including, but not limited to, amino groups, carboxyl groups, oxo groups or thiol groups. Using these functional groups, the probes may be attached using functional groups on the probes either directly or indirectly using a linkers. The probes may be attached to the solid support by either the 5′ terminus, 3′ terminus, or via an internal nucleotide. The probe may also be attached to the solid support non-covalently. For example, biotinylated oligonucleotides can be made, which may bind to surfaces covalently coated with streptavidin, resulting in attachment. Alternatively, probes may be synthesized on the surface using techniques such as photopolymerization and photolithography.

miRNA Expression Analysis.

miRNAs that are associated with disease or a pathological condition can be identified. A biological sample can be contacted with a probe or microarray of the invention and the amount of hybridization determined. PCR may be used to amplify nucleic acids in the sample, which may provide higher sensitivity.

The ability to identify miRNAs that are overexpressed or underexpressed in pathological cells compared to a control can provide high-resolution, high-sensitivity datasets which may be used in the areas of diagnostics, therapeutics, drug development, pharmacogenetics, biosensor development, and other related areas. An expression profile may be a “fingerprint” of the state of the sample with respect to a number of miRNAs. While two states may have any particular miRNA similarly expressed, the evaluation of a number of miRNAs simultaneously allows the generation of a gene expression profile that is characteristic of the state of the cell. That is, normal tissue may be distinguished from diseased tissue. By comparing expression profiles of tissue in known different disease states, information regarding which miRNAs are associated with each of these states may be obtained. This provides a molecular diagnosis of related conditions.

Determining Expression Levels.

Expression level of a disease-associated miRNA can be determined. A biological sample can be contacted with a probe or microarray of the invention and the amount of hybridization determined. The expression level of a disease-associated miRNA can be used in a number of ways. For example, differential expression of a disease-associated miRNA compared to a control may be used as a diagnostic that a patient suffers from the disease. Expression levels of a disease-associated miRNA may also be used to monitor the treatment and disease state of a patient. Furthermore, expression levels of a disease-associated miRNA allows the screening of drug candidates for altering a particular expression profile or suppressing an expression profile associated with disease. Differential expression is determined if the differences are statistically significant.

A target nucleic acid may be detected by contacting a sample comprising the target nucleic acid with a microarray comprising an attached probe sufficiently complementary to the target nucleic acid and detecting hybridization to the probe above control levels. The target nucleic acid may also be detected by immobilizing the nucleic acid to be examined on a solid support such as nylon membranes and hybridizing a labeled probe with the sample. Similarly, the target nucleic may also be detected by immobilizing the labeled probe to the solid support and hybridizing a sample comprising a labeled target nucleic acid. Following washing to remove the non-specific hybridization, the label may be detected.

A target nucleic acid may also be detected in situ by contacting permeabilized cells or tissue samples with a labeled probe to allow hybridization with the target nucleic acid. Following washing to remove the non-specifically bound probe, the label may be detected. Such hybridization assays can be direct hybridization assays or can comprise sandwich assays, which include the use of multiple probes, as is generally outlined in U.S. Pat. Nos. 5,681,702; 5,597,909; 5,545,730; 5,594,117; 5,591,584; 5,571,670; 5,580,731; 5,571,670; 5,591,584; 5,624,802; 5,635,352; 5,594,118; 5,359,100; 5,124,246; and 5,681,697, each of which is hereby incorporated by reference.

A variety of hybridization conditions may be used, including high, moderate and low stringency conditions. The assays may be performed under stringency conditions which allow hybridization of the probe only to the target. Stringency can be controlled by altering a parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaotropic salt concentration pH, or organic solvent concentration.

Hybridization reactions may be accomplished in a variety of ways. Components of the reaction may be added simultaneously, or sequentially, in different orders. In addition, the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g., albumin, detergents, etc. which may be used to facilitate optimal hybridization and detection, and/or reduce non-specific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors and anti-microbial agents may also be used as appropriate, depending on the sample preparation methods and purity of the target.

Diagnostic Assays.

A differential expression level of a disease-associated miRNA in a biological sample can be determined. The sample may be derived from a patient, and may be a body fluid or a tissue sample. Diagnosis of a disease state in a patient allows for prognosis and selection of therapeutic strategy. Further, the developmental stage of cells may be classified by determining temporally expressed miRNA-molecules.

In situ hybridization of labeled probes to tissue arrays may be performed. When comparing the fingerprints between an individual and a standard, the skilled artisan can make a diagnosis, a prognosis, or a prediction based on the findings. It is further understood that the genes which indicate the diagnosis may be the same or differ from those which indicate the prognosis. Molecular profiling of the condition of the cells may lead to distinctions between responsive or refractory conditions or may be predictive of outcomes.

Drug Screening.

The present invention also relates to a method of screening therapeutics comprising contacting a pathological cell capable of expressing a disease related miRNA with a candidate therapeutic and evaluating the effect of a drug candidate on the expression profile of the disease associated miRNA. Having identified the differentially expressed miRNAs, a variety of assays may be executed. Test compounds may be screened for the ability to modulate gene expression of the disease associated miRNA. Modulation includes both an increase and a decrease in gene expression. Test can be conducted in any type of cell, including but not limited to human cells, human cell lines, mammalian cells and cell lines, mammalian cancer cells and cell lines.

The test compound or drug candidate may be any molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or indirectly alter the disease phenotype or the expression of the disease associated miRNA. Drug candidates encompass numerous chemical classes, such as small organic molecules having a molecular weight of more than 100 and less than about 500, 1,000, 1,500, 2,000, or 2,500 daltons. Candidate compounds may comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents may comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.

Combinatorial libraries of potential modulators may be screened for the ability to bind to the disease associated miRNA or to modulate the activity thereof. The combinatorial library may be a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical building blocks such as reagents. Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries encoded peptides, benzodiazepines, diversomers such as hydantoins, benzodiazepines and dipeptide, vinylogous polypeptides, analogous organic syntheses of small compound libraries, oligocarbamates, and/or peptidyl phosphonates, nucleic acid libraries, peptide nucleic acid libraries, antibody libraries, carbohydrate libraries, and small organic molecule libraries.

Gene Silencing.

The present invention also relates to a method of using the nucleic acids of the invention to reduce expression of a target gene in a cell, tissue or organ. Expression of the target gene may be reduced by expressing a nucleic acid of the invention that comprises a sequence substantially complementary to one or more binding sites of the target mRNA. The nucleic acid may be a miRNA or a variant thereof. The nucleic acid may also be pri-miRNA, pre-miRNA, or a variant thereof, which may be processed to yield a miRNA. The expressed miRNA may hybridize to a substantially complementary binding site on the target mRNA, which may lead to activation of RISC-mediated gene silencing. An example for a study employing over-expression of miRNA is Yekta et al. 2004, Science, 304-594, which is incorporated herein by reference. One of ordinary skill in the art will recognize that the nucleic acids of the present invention may be used to inhibit expression of target genes using antisense methods well known in the art, as well as RNAi methods described in U.S. Pat. Nos. 6,506,559 and 6,573,099, which are incorporated by reference. The target of gene silencing may be a protein that causes the silencing of a second protein. By repressing expression of the target gene, expression of the second protein may be increased. Examples for efficient suppression of miRNA expression are the studies by Esau et al 2004 JBC 275-52361; and Cheng et al 2005 Nucleic Acids Res. 33-1290, which is incorporated herein by reference.

Gene Enhancement.

The present invention also relates to a method of using the nucleic acids of the invention to increase expression of a target gene in a cell, tissue or organ. Expression of the target gene may be increased by expressing a nucleic acid of the invention that comprises a sequence substantially complementary to a pri-miRNA, pre-miRNA, miRNA or a variant thereof. The nucleic acid may be an anti-miRNA. The anti-miRNA may hybridize with a pri-miRNA, pre-miRNA or miRNA, thereby reducing its gene repression activity. Expression of the target gene may also be increased by expressing a nucleic acid of the invention that is substantially complementary to a portion of the binding site in the target gene, such that binding of the nucleic acid to the binding site may prevent miRNA binding.

Therapeutic.

The present invention also relates to a method of using the nucleic acids of the invention as modulators or targets of disease or disorders associated with developmental dysfunctions, such as cancer. In general, the claimed nucleic acid molecules may be used as a modulator of the expression of genes which are at least partially complementary to said nucleic acid. Further, miRNA molecules may act as target for therapeutic screening procedures, e.g., inhibition or activation of miRNA molecules might modulate a cellular differentiation process, e.g. apoptosis.

Furthermore, existing miRNA molecules may be used as starting materials for the manufacture of sequence-modified miRNA molecules, in order to modify the target-specificity thereof, e.g., an oncogene, a multidrug-resistance gene or another therapeutic target gene. Further, miRNA molecules can be modified, in order that they are processed and then generated as double-stranded siRNAs which are again directed against therapeutically relevant targets. Furthermore, miRNA molecules may be used for tissue reprogramming procedures, e.g., a differentiated cell line might be transformed by expression of miRNA molecules into a different cell type or a stem cell.

Compositions.

The present invention also relates to a pharmaceutical composition comprising the nucleic acids of the invention and optionally a pharmaceutically acceptable carrier. The compositions may be used for diagnostic or therapeutic applications. The administration of the pharmaceutical composition may be carried out by known methods, wherein a nucleic acid is introduced into a desired target cell in vitro or in vivo. Commonly used gene transfer techniques include calcium phosphate, DEAE-dextran, electroporation, microinjection, viral methods and cationic liposomes.

Kits.

Kits may comprise a nucleic acid of the invention together with any or all of the following: assay reagents, buffers, probes and/or primers, and sterile saline or another pharmaceutically acceptable emulsion and suspension base. In addition, the kits may include instructional materials containing directions (e.g., protocols) for the practice of the methods of this invention.

Subjects.

Subjects can be mammals, such as humans, monkeys, rats, mice, dogs, cats, guinea pigs, pigs, etc. The humans can be those who are known to have cancer or are suspected of having cancer. The cancer may have been previously treated or not. The cancer may be colorectal, lung, breast, stomach, kidney, ovarian, bladder, head and neck, brain, bone, testicular, pancreatic, prostate, etc.

The above disclosure generally describes the present invention. All references disclosed herein are expressly incorporated by reference. A more complete understanding can be obtained by reference to the following specific examples which are provided herein for purposes of illustration only, and are not intended to limit the scope of the invention.

EXAMPLE 1 Materials and Methods

Cell Culture and Colorectal Tissue.

Colorectal cancer cell lines HCT116, DLD1, RKO, CACO-2, SW480, and their derivatives were cultured in McCoy's SA medium supplemented with 10% FCS and penicillin/streptomycin. Samples of colorectal cancer tissue and matched normal colonic epithelium were obtained from patients undergoing surgery and were frozen immediately (<10 min) after surgical resection. Acquisition of tissue specimens was performed in accordance with Health Insurance Portability and Accountability Act of 1996 (HIPAA) regulations.

RNA, DNA, and RNA/DNA Oligonucleotides.

RNA and RNA/DNA oligonucleotides were obtained from Dharmacon Research (Lafayette, Colo.). Deoxyribonucleotides are preceded by a “d.” miRAGE 3′ linker: 5′-phosphate-UCUCGAGGUACAUCGUUdAdGdAdAdGdCdTdTdGdAdAdTdTdCdGdAdGdCd AdGdAdAdAN3-3′ (SEQ ID NO: 1875); miRAGE 5′ linker: 5′-dTdTdTdGdGdAdTdTdTdGdCdTdGdGdTdGdCdAdGdTdAdCdAdAdCdTdAdGdGd CdTdTdACUCGAGC(SEQ ID NO: 1876); 18-base RNA standard: 5′-phosphate-ACGUUGCACUCUGAUACC (SEQ ID NO: 1877); 26-base RNA standard: 5′-phosphate-CCGGUUCAUCACGUCUAAGAAUCAUG (SEQ ID NO: 1878). DNA oligonucleotides were obtained from Integrated DNA Technologies (San Jose, Calif.). miRAGE reverse transcription primer: 5′-TTTCTGCTCGAATTCAAGCTTCT (SEQ ID NO: 1879); LongSage PCR primer (forward): 5′-biotin-TTTTTTTTTGGATTTGCTGGTGCAGTACA-3′(SEQ ID NO: 1880); LongSage PCR primer (reverse): 5′-biotin-TTTTTTTTTCTGCTCGAATTCAAGCTTCT-3′(SEQ ID NO: 1881).

miRAGE Approach for miRNA Identification. Step 1: 18- to 26-Bp RNA Isolation and Linker Ligation.

Total RNA was isolated from cell lines/tissue samples by using the RNagents kit (Prornega) following the manufacturer's protocol, with the exception that no final 75% ethanol wash was performed. RNA of the 18- to 26-base size range was isolated by electrophoresing 1 mg of total RNA alongside 18- and 26-base RNA standards on two 15% polyacrylamide TBE/Urea Novex gels (Invitrogen) at 180 V for 70 min. The 18- and 26-base RNA standards were carried through all subsequent ligation steps to serve as size standards for gel purification. RNAs ranging from 18 to 26 bases in length were visualized with SYBR Gold Nucleic Acid Gel Stain (Molecular Probes), excised from the gel, pulverized by spinning at high speed through an 18-gauge needle-pierced centrifuge tube, and gel-extracted by incubating the gel slices in 0.3 M NaCl at 4° C. on a rotisserie-style rotator for 5 h. The contents were then transferred into a Costar Spin-X Centrifuge Tube Filter (VWR Scientific), spun into a fresh tube, EtOH-precipitated (by adding 3 volumes of 100% EtOH), and resuspended in water. Small RNAs were subsequently dephosphorylated with calf intestinal alkaline phosphatase (NEB, Beverly, Mass.) at 50° C. for 30 min, phenol/chloroform-extracted, re-EtOH precipitated, and ligated to the miRAGE 3′ Linker with T4 RNA ligase (NEB) at 37° C. for 1 h. After gel purification of 58- to 66-base RNA products and EtOH precipitation (as described above), the samples were phosphorylated with T4 polynucleotide kinase (NEB) at 37° C. for 30 min, phenol/chloroform-extracted, EtOH-precipitated, and ligated (as above) to the miRAGE 5′ Linker.

Step 2: Tag Amplification, Isolation, Concatenation, Cloning, and Sequencing.

After gel purification of RNA products ranging from 98 to 106 bases, reverse transcription of the ligation products was performed by using miRAGE reverse transcription primer and SuperScript II RT (Invitrogen) for 50 min at 45° C. Subsequently, the procedures for amplifying, isolating, purifying, concatenating, cloning, and sequencing tags are nearly identical to those performed in LongSAGE and Digital Karyotyping, except that miRAGE PCR products range in size from 110 to 118 bp, and miRAGE tags (not ditags) were released from linkers with XhoI endonuclease (NEB). The sequencing of concatemer clones was performed by contract sequencing at Agencourt (Beverly, Mass.). Resulting sequence files were trimmed by using PHRED sequence analysis software (CodonCode, Dedham, Mass.), and 18- to 26-bp tags were extracted by using the SAGE2000 software package, which identifies the fragmenting enzyme site between tags, extracts intervening tags, and records them in a database.

Bioinformatic Analyses of miRAGE Tags. Step 1; Grouping and Comparing miRAGE Tags to Known RNAs.

All tags sharing a common set of 11 of 12 core internal sequence elements were assembled into groups containing all related members. The tag with the most counts in each group was further analyzed. Grouping facilitated analysis by (i) eliminating rare sequencing errors and (ii) removing trivial miRNA variants, because miRNAs are known to display both 5′ and 3′ variation. The tags were subsequently compared to databases of known RNA sequences (miRNAs, mRNAs, rRNAs, etc.), using BLAST, and those tags matching known sequences were removed from further analysis. The tags obtained by miRAGE were compared with public databases on Sep. 1, 2005. Subsequent additions and changes to these databases are not reflected in the data analysis.

Step 2: Secondary Structure Analysis and Hairpin Stability Scoring of Candidate miRNAs.

To determine potential miRNA precursor structures, each tag was compared to the human genome sequence. For tags with perfect matches, a total of 75 bp (60+15 bp) of flanking genomic sequence around each tag was extracted. Because there are two possible precursors for each tag (i.e., the tag can be located on the 5′ or 3′ arm of a putative hairpin), pairs of theoretical precursors were extracted from the human genome at the position of each tag and were carried through the following analysis. Secondary structure and free energy of folding were determined for each pair of precursor structures by using MFOLD 3.2 (26, 27) and compared to values obtained for known miRNAs. The values used for thermodynamic evaluation were the free energy of folding of each precursor sequence (ΔG_(folding)) and the difference of ΔG_(folding) between the two possible precursors (ΔΔG_(folding)). Analysis of an arbitrary set of 126 known miRNAs using these thermodynamic analyses revealed that the highest ΔG_(folding) was −22.6, and there were no miRNAs with a ΔG_(folding)>−29.0, which had a ΔΔG_(folding)<5. Therefore, for a candidate miRNA precursor structure to be considered legitimate, it would have to have either (i) ΔG_(folding)≦−29 or (ii) −29<ΔG_(folding)≦−22 and ΔΔG_(folding)>5. In cases where both precursors fulfilled these criteria, the member of each pair with the lowest ΔG_(folding) was further considered. Precursors that had not been excluded up to this point were subsequently analyzed to determine whether they conformed to generally acceptable miRNA base-pairing standards (base-pairing involving at least 16 of the first 22 nucleotides of the miRNA and the other arm of the hairpin) (18).

Step 3: Determination of Hairpin Conservation.

We classified all candidate miRNAs as either “conserved” or “nonconserved” by using the University of California at Santa Cruz phastCons database (28). This database has scores at each nucleotide in the human genome that correspond to the degree of conservation of that particular nucleotide in chimpanzee, mouse, rat, dog, chicken, pufferfish, and zebrafish. The algorithm is based on a phylogenetic hidden Markov model using best-in-genome pairwise alignment for each species (based on BLASTZ), followed by multialignment of the eight genomes. A hairpin was defined as conserved if the average phastCons conservation score over the seven species in any 15-nt sequence in the hairpin stem is at least 0.9 (5, 29).

Determination of Homology of Candidate miRNAs to Existing miRNAs.

One hundred random 22 mers were generated and compared to the miRBase database using the SSEARCH search algorithm, and expect values were obtained for each. E values for randomly generated sequences ranged from 0.07 to 23. All 133 miRNA candidates were subsequently analyzed, and tags with E values <0.05 were deemed to have homology to existing miRNAs.

miRNA Microarray Expression Analysis.

Five micrograms of total RNA from human placenta, prostate, testes, and brain (Ambion, Austin, Tex.) were size-fractionated (<200 nt) by using the mirVana kit (Ambion) and labeled with Cy3 (placenta and testes) and Cy5 (prostate and brain) fluorescent dyes. Pairs of labeled samples were hybridized to dual-channel microarrays. Microarray assays were performed on a μParaFlo microfluidics microarray with each of the detection probes containing a nucleotide sequence of coding segment complementary to a specific microRNA sequence and a long nonnucleotide molecule spacer that extended the detection probe away from the substrate. The melting temperature of the detection probes was balanced by incorporation of varying number of modified nucleotides with increased binding affinities. The maximal signal level of background probes was 180. A miRNA detection signal threshold was defined as twice the maximal background signal.

Quantitative RT-PCR (qRT-PCR) Expression Analysis.

qRT-PCRs were performed by using SuperTaq Polymerase (Ambion) and the mirVana qRT-PCR miRNA Detection Kit (Ambion) following the manufacturer's instructions. Reactions contained custom-designed oligonucleotide DNA primers (Integrated DNA Technologies) specific for 36 novel putative miRNAs or mirVana qRT-PCR Primer Sets specific for hsa-miR-16, hsa-miR-24, hsa-miR-143, or human 5S rRNA as positive controls. For each set of primers, 100 ng of FirstChoice human colon Tumor/Normal Adjacent Tissue RNA (Ambion); a pool containing 50 ng of HCT116, RKO, and DLD-1 cell lines total RNA; a pool containing 50 ng of FirstChoice Total RNA from human brain, cervix, thymus, and skeletal muscle (Ambion); and a no-template negative control were tested. All RNAs were treated with TURBO DNase. qRT-PCR was performed on an ABI7000 thermocycler (Applied Biosciences), and end-point reaction products were also analyzed on a 3.5% high-resolution agarose gel (Ambion) stained with ethidium bromide to discriminate between the correct amplification products (≈90 bp) and the potential primer dimers.

Targeted Disruption of the Human Dicer Locus.

The strategy for creating knockouts with AAV vectors was performed as described (30, 31). The targeting construct pAAV-Neo-Dicer was made by PCR, by using bacterial artificial chromosome clone CITB 2240H23 (Invitrogen) as the template for the homology arms. A targeted insertion was made in exon 5, which is part of the helicase domain. Details of the vector design and sequences of all PCR primers are available from the authors upon request. Stable G418-resistant clones were initially selected in the presence of Geneticin (Invitrogen), then routinely propagated in the absence of selective agents.

Determination of Differential Expression.

Tag numbers from the different libraries were normalized and compared by using a Fisher exact test (significance threshold P=0.05) with Bonferroni correction (32).

EXAMPLE 2 Genome-Wide miRNA Analysis with miRAGE

Using miRAGE, we analyzed 273,966 cDNA tags obtained from four human colorectal cancers and two matching samples of normal colonic mucosae. Comparing these tags to the existing miRNA database identified 68,376 tags matching known miRNA sequences. These represent the largest collection of human miRNA sequences identified to date, because all previous human miRNA cloning analyses in aggregate have analyzed <2,000 miRNA molecules. The expression level of the miRNAs detected by miRAGE ranged over 4 orders of magnitude (from 23,431 observations for miR-21 to 20 miRNAs that were observed only once), suggesting this approach can detect miRNAs present at varied expression levels. The identified miRNA tags matched 200 of the mature miRNAs present in the public miRBase database (2) (Table 2, which is published as supporting information on the PNAS web site), and 52 of these were expressed at significantly different levels between tumor cells and normal colonic epithelium (P<0.05, Fisher exact test; Table 3, which is published as supporting information on the PNAS web site). Importantly, of the already catalogued miRNAs, these results provide novel experimental evidence for 62 miRNAs whose presence in this database was based solely on phylogenetic predictions.

In addition to detecting known or predicted miRNAs, 1,411 of the miRAGE tags represented 100 previously unrecognized miRNA* forms of known miRNAs (Table 4, which is published as supporting information on the PNAS web site). miRNA* molecules correspond to the short-lived complementary strand present in initial miRNA duplexes, and their biologic role, if any, has yet to be elucidated. Although miRNA* have been inferred to exist for all miRNAs, only 24 human miRNAs* have previously been reported in the public database. These analyses therefore provide substantially greater evidence for the presence of these molecules in human cells

EXAMPLE 3 Evaluation of Novel miRNAs

We next focused on evaluating whether the miRAGE tags not matching known miRNAs might represent novel miRNA species. As a first step, miRAGE tags were compared with existing gene databases to exclude sequences matching known RNAs, including noncoding RNAs, mRNAs, and RNAs derived from mitochondrial sequences (FIG. 1B). The remaining tags were then evaluated in silico for the ability of their putative precursor sequences to form hairpin structures that were thermodynamically stable. The miRAGE approach in combination with these steps were expected to fulfill both the “expression” and “biogenesis” criteria recently put forward by Ambros et al. (18) in an effort to maintain a uniform system for miRNA annotation. Using these criteria, a total of 168 tags were identified that corresponded to putative novel miRNAs.

EXAMPLE 4 Validation of Novel miRNAs

During the course of our study, 35 of these 168 miRAGE tags were independently identified by using a combination of bioinformatic and expression analyses (5). These findings provide a separate measure of validation of the miRAGE approach for miRNA identification. Several lines of evidence suggested that most of remaining 133 miRAGE tags also corresponded to previously uncharacterized miRNAs (Table 5, which is published as supporting information on the PNAS web site). First, phylogenetic conservation was determined for each tag precursor structure with respect to chimpanzee, mouse, rat, dog, chicken, pufferfish, and zebrafish genomes. A total of 32 of the 133 candidate miRNAs had conserved precursor structures. Furthermore, six of the miRNA candidates showed significant homology to the mature miRNA sequence of known miRNAs. Although these observations provide support for evolutionarily conserved novel miRNAs, they should not be used to exclude the remaining tags as legitimate miRNAs, because a significant number of recently reported human miRNAs lack homology to species other than primates (5). Second, 81 of the novel candidate miRNAs were represented by more than one miRAGE tag or were independently detected in additional samples by using either miRNA microarrays (5, 19) (Table 6, which is published as supporting information on the PNAS web site) or quantitative real-time PCR (Table 7 and FIG. 7, which are published as supporting information on the PNAS web site). Third, 15 of the candidate miRNAs were localized to genomic clusters of two or more miRNAs separated by an average distance of 10 kb (FIG. 2). This physical proximity is consistent with recent reports of miRNAs clustering within the human genome (20). Fourth, identification of a corresponding miRNA* sequence (with characteristic 3′ overhangs) to a particular miRNA is a strong indicator that the small RNA species in question was processed by an RNase III enzyme such as Dicer. miRNA* tags were observed for 12 of the candidate miRNA sequences. In total, 89 of the 133 novel candidate miRNAs had at least one independent piece of supporting evidence buttressing their legitimacy (FIG. 3).

As a separate experimental approach to validate candidate miRNAs, we examined whether the generation of these small RNAs depended on Dicer processing. The rationale for this analysis was based on the fact that Dicer-depleted cells contain reduced amounts of mature miRNAs (18). However, because Dicer−/−vertebrate cells have been shown to be inviable (21), we sought to generate a Dicer mutant line displaying a hypomorphic phenotype. Such a mutant has been reported in mouse studies targeting the N terminus of Dicer (22). Accordingly, we disrupted exon 5 of the human Dicer gene by using an AAV targeting construct, thereby interrupting a well conserved segment of the N-terminal helicase domain while sparing the RNase III domains. The helicase domain was successfully disrupted by this approach in three different colorectal cancer cell lines (FIG. 4).

Analysis of selected miRNA genes from all three Dicer exon 5-disrupted lines (hereafter referred to as Dicer^(ex5)) revealed reduced amounts of mature miRNAs and accumulation of miRNA precursors, when compared to their corresponding parental lines (FIGS. 5A and B). miRAGE was then performed on both HCT116 wild type and HCT-Dicer^(ex5) cells to quantify differences of known and novel miRNA levels. Of 97 known miRNAs detected in these two cell lines, 55 were differentially expressed, and for 53 of these 55, there was an average 7-fold reduction of miRNA levels in Dicer^(ex5) cells compared with wild-type cells (Table 8, which is published as supporting information on the PNAS web site). Examination of the 168 candidate miRNAs similarly revealed that among the six candidates that were differentially expressed, there was an average 14-fold reduction of miRNA levels in Dicer^(ex5) cells (Table 1). These observations are consistent with the conclusion that Dicer is required for the biogenesis of a subset of known and novel miRNAs.

EXAMPLE 5 Target Genes

The miRNAs were used to predict target genes and their binding. Table 9 (FIG. 16) lists the predicted target gene for each miRNA. The names of the target genes were taken from NCBI Reference Sequence release 9 (http://www.ncbi_nlm.nih.gov; Pruitt et al., Nucleic Acids Res, 33(1): D501-D504, 2005; Pruitt et al., Trends Genet., 16(1): 44-47, 2000; and Tatusova et al., Bioinformatics, 15(7-8): 536-43, 1999). Target genes were identified by having a perfect complimentary match of a 7 nucleotide miRNA seed (positions 2-8) that have an “A” in the UTR opposite to position 1 of the miRNA, except in one case, hsa-mir-560, for which the binding site does not have an “A” in that position. For a discussion on identifying target genes, see Lewis et al., Cell, 120: 15-20, (2005). For a discussion of the seed being sufficient for binding of a miRNA to a UTR, see Lim et al., (Nature, 2005, 433:769-773) and Brenneck et al, (PLoS Biol, 2005, (3): e85).

Binding sites were predicted on genes whose UTR is of at least 30 nucleotides. In addition, the binding site screen only considered the first 8000 nucleotides per UTR and considered the longest transcript when there were several transcripts per gene. A total of 14,236 transcripts were included in the dataset. Table 9 [FIG. 16] lists the predicted binding sites for each target gene as predicted from each miRNA. The sequence of the binding site includes the 20 nucleotides 5′ and 3′ away from the binding site as they are located on the spliced mRNA.

EXAMPLE 6 Concluding Remarks

Our studies have provided experimental evidence that the human genome contains a much larger number of miRNAs than previously appreciated (4). To determine the rate at which uncharacterized miRNAs are likely to be discovered by using miRAGE, we simulated the number of miRNAs species that would have been detected by using subsets of the tags analyzed (FIG. 6). Although the number of known miRNAs clearly plateaus after analysis of ≈50,000 tags, the number of novel miRNAs appears to increase linearly even at ≈270,000 tags. These observations suggest many novel miRNAs remain to be identified.

The tools we have developed, miRAGE and the Dicer^(ex5) cells with defective miRNA processing, should provide a facile way to identify and validate novel miRNAs. As new lower-cost sequencing methods continue to be developed (23-25), this approach will become progressively more useful for the discovery of the compendium of miRNAs present in humans and other organisms.

REFERENCES

The disclosure of each reference cited is expressly incorporated herein.

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The invention claimed is:
 1. A method comprising: assaying and detecting presence of an miRNA having SEQ ID NO: 458 in a body fluid or tumor specimen from a patient by contacting and hybridizing a probe attached to a solid support with nucleic acids of the body fluid or tumor specimen, wherein the probe is complementary to SEQ ID NO: 458, wherein the miRNA is expressed in tumor tissue or cell lines but not in normal tissue of the patient.
 2. A method of diagnosing a cancer in a patient comprising: assaying and detecting presence of an miRNA of SEQ ID NO: 458 in a body fluid or tumor specimen from the patient, wherein the miRNA is expressed in tumor tissue but not in normal tissue of the patient, wherein the assaying comprises contacting the body fluid or tumor specimen with a hybridization probe complementary to SEQ ID NO: 458 attached to a solid support; and identifying a cancer in the patient when the miRNA is detected in the body fluid or tumor specimen.
 3. The method of claim 1 wherein the solid support is a microarray.
 4. The method of claim 1 wherein the hybridization probe is labelled.
 5. The method of claim 1 wherein the miRNA or its miRNA precursor is labelled.
 6. A method of diagnosing a cancer in a patient comprising: detecting presence of a labelled miRNA of SEQ ID NO: 458 in a body fluid or tumor specimen from the patient by contacting and hybridizing a probe attached to a solid support with nucleic acids of the body fluid or tumor specimen, wherein the probe is complementary to SEQ ID NO: 458, wherein miRNA of SEQ ID NO: 458 or its miRNA precursor is expressed in tumor tissue or cell lines but not in normal tissue; and identifying a cancer in the patient.
 7. The method of claim 2 wherein the solid support is a microarray.
 8. The method of claim 2 wherein the hybridization probe is labelled.
 9. The method of claim 6 wherein the solid support is a microarray.
 10. The method of claim 6 wherein the hybridization probe is labelled. 